annotate biotranslator.xml @ 15:97abe4dc3ee3 draft

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author enios
date Sat, 22 May 2021 07:30:24 +0000
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1 <tool id="biotranslator" name="biotranslator" >
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2 <requirements>
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3 <container type="docker">eniosorg/bim:biotranslator_</container>
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4 </requirements>
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5 <description>** Biotranslator **</description>
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6 <command><![CDATA[ python /code/wrapper.py
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7 --authtoken $authtoken
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8 --dataset $dataset
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9 --project $project
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10 --idtype '$id_type'
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11 --organism '$organism'
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12 --terms '$terms'
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13 --foldchange '$fold_change'
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14 --correctedpvalue '$correctedpvalue'
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15 --title '$exp_title'
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16 --description '$description'
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17 && cp *.html $html
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18 && tar -cvf $results *
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19 ]]></command>
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20 <inputs>
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21 <param type="text" name="authtoken" value="7dajfghfhjs7fgh" label="Give your bionfominer authentication token "/>
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22 <param type="float" name="correctedpvalue" value="0.05" label="correctedpvalue"/>
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23 <param type="data" name="dataset" format="csv,txt,tabular,semicolon" label="gene list file"/>
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24 <param type="text" name="description" value="description" label="description"/>
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25 <param type="text" name="exp_title" value="exp_title" label="exp_title"/>
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26 <param type="select" name="fold_change" value="None" label="foldchange">
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27 <option value="None">None</option>
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28 <option value="Log">Log</option>
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29 <option value="Linear">Linear</option>
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30 </param>
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31 <param type="select" name="organism" value="Homo sapiens" label="organism">
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32 <option value="Homo sapiens">Homo sapiens</option>
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33 <option value="Mus musculus">Mus musculus</option>
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34 <option value="Rattus novergicus">Rattus novergicus</option>
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35 <option value="Bos taurus">Bos taurus</option>
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36 <option value="Sus scrofa">Sus scrofa</option>
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37 <option value="Gallus gallus">Gallus gallus</option>
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38 <option value="Danio rerio">Danio rerio</option>
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39 <option value="Drosophila melanogaster">Drosophila melanogaster</option>
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40 <option value="Caenorhabditis elegans">Caenorhabditis elegans</option>
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41 <option value="Saccharomyses serevisiae">Saccharomyses serevisiae</option>
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42 <option value="Schizosaccharomyses pombe">Schizosaccharomyses pombe</option>
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43 <option value="Aspergillus nidulans">Aspergillus nidulans</option>
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44 <option value="Magnaporthe grisea">Magnaporthe grisea</option>
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45 <option value="Arabidopsis thaliana">Arabidopsis thaliana</option>
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46 <option value="Oryza sativa Japonica">Oryza sativa Japonica</option>
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47 <option value="Glycine max">Glycine max</option>
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48 <option value="Hellanthus annuus">Hellanthus annuus</option>
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49 <option value="Sorghum bicolor">Sorghum bicolor</option>
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50 <option value="Zea mays">Zea mays</option>
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51 <option value="Beta vulgaris">Beta vulgaris</option>
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52 </param>
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53 <param type="select" name="id_type" value="Gene Symbol" label="Id type">
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54 <option value="Gene Symbol">Gene Symbol</option>
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55 <option value="Entrez Gene id">Entrez Gene id</option>
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56 <option value="Ensembl Gene id">Ensembl Gene id</option>
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57 </param>
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58 <param type="text" name="project" value="hgjahgdf7886sjhfg" label="Provide a bioinfominer project ID"/>
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59 <param type="select" name="terms" value="Gene Ontology" label="terms">
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60 <option value="Gene Ontology">Gene Ontology</option>
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61 <option value="MGI Mammalian Phenotype">MGI Mammalian Phenotype</option>
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62 <option value="Human Phenotype Ontology">Human Phenotype Ontology</option>
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63 <option value="Plant Ontology">Plant Ontology</option>
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64 <option value="Zebrafish Ontology">Zebrafish Ontology</option>
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65 </param>
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66 </inputs>
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67 <outputs>
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68 <data name="html" format="html" />
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69 <data name="results" format="tar" />
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70 <!--data name="analysis" format="tsv" />
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71 <data name="extended_analysis" format="txt" />
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72 <data name="visualization" format="html" /-->
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73 </outputs>
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74 </tool>